The Apollinar and its successors can closely be linked to the site next to the theatre due to Ascanius's reference[2] to it being "outside the porta Carmentalis between the Forum Holitorium and the Circus Flaminius", Livy's placing it in the prata Flaminia (Flaminian meadows, as this area was then called)[3] and other references placing it near to the forum,[4] the Capitol[5] and the theatre of Marcellus[6] respectively. All these indicate the presently-accepted site for this temple, just north of the theatre and east of the porticus Octaviae, on the street leading through the porta Carmentalis to the campus Martius, a little south of the present Piazza Campitelli.

The three columns of the temple which survive to full-height today belong to the Augustan rebuild, but the cult of Apollo had existed in this area since at least to the mid-5th century BC when an Apollinar (a sacred grove or altar) was recorded on this site. Since Apollo was a foreign cult, it thus legally had to be placed outside the pomerium,[7] making it a regular spot for extra-pomerial senate meetings[8] (This was also Apollo's only temple in Rome until Augustus dedicated another on the Palatine Hill.)[9]

The first temple building dates to 431 BC, when the consul Gnaeus Iulius Mento inaugurated one dedicated to Apollo Medicus (the doctor), in fulfilment of a vow to him during a plague of 433 BC.[10] This building was restored in 353 BC,[11] and perhaps in 179 BC, when the censor Marcus Aemilius Lepidus and his colleague let the contract for building a porticus from the temple to the Tiber, behind the temple of Spes[12] The censor's projects also included a nearby theatre. The shedding of tears for three days by a cult-statue of Apollo, cited among the prodigies at the death of the Younger Scipio,[13] can only have occurred at this temple, there being no others to Apollo.

A neighbouring temple dedicated to Apollo's sister Diana probably dates to the late Republic, following the destruction of the Apollo temple's precinct in work on the theatre of Marcellus.

A radical reconstruction was begun by Gaius Sosius, probably just after his triumph in 34 BC.[14] These building-works were themselves soon interrupted by the civil war between Octavian and Antony (with Sosius taking Antony's side), and only resumed some years later when Augustus was reconciled with Sosius. It was thus dedicated in the end to the name of the princeps, with the dedication day in the Augustan period of 23 September.[15] Upon the construction of the theatre of Marcellus soon afterwards the temple's frontal staircase was demolished and replaced with two staircases on the sides of the "pronaos".

The temple's ruins were occupied in the post-Roman period by medieval dwellings right up to the 1930s, when these were demolished between 1926 and 1932 to allow the theatre of Marcellus to be seen in isolation. In those same works the remains of the fallen colonnade were recovered in the very positions in which they had fallen, inside the arches of the theatre and as a result in 1937 and 1938 the podium's remains were excavated. In 1940 the fallen columns were raised on this podium, though probably not in their original positions.

The building is oriented almost perfectly towards the south, differing from the orientation of the other neighbouring buildings, including the adjoining temple of Bellona.

The Augustan phase of the temple was made up of a podium under the columns and the cella walls, with its supporting parts made up of travertine blocks to carry the weight and the non-supporting parts merely of tuff blocks and cement. The remains of the podium wall surviving beneath the cloisters of Santa Maria in Campitelli - 13 metres long, over 4 high and over 2 thick - were assumed by Delbrück to be unquestionably a part of the original structure.[23] Frank, however, maintains that though the cappellaccio tuff core may belong to the original building, the rest (besides some concrete with an opus reticulatum facing, attributable to the 34 BC phase) belongs to the 179 BC restoration. He argues this from the use in the remains' facing of tuff from Monte Verde, the southern end of the Janiculum Hill.[24]

The temple's hexastyle elevation was formed of Carrara marble columns along the front and the two long sides of the pronaos, with those at the back made of plastered brick. This style was continued in travertine half-columns (plastered to look like marble) against the cella walls.

The facade's architrave was made up of blocks of travertine faced and supported with marble in the pittabanda style, rather than solid blocks of marble alone. In the same way the frieze was sculpted on slabs placed on the supporting structure. The capitals are corinthian with extra vegetable motifs (in Italian, "corinzieggiante", no English equivalent), and the frame presents a very protruding ceiling supported by brackets.

The temple's main pediment was decorated with sculptures removed from a classical temple in Greece. These date to c. 450 - 425 BC and show an amazonomachy. They are now preserved at Centrale Montemartini of the Capitoline Museums.

The cella's interior walls were decorated with a double order of column shafts in African marble, the lower one with a frieze representing stages of the battles included in the triple triumph of Octavian in 29 BC. Between the columns were aediculae with column-shafts in different coloured marbles (giallo antico, pavonazzetto and portasanta) and with tympana in unusual shapes (triangular, half-moon and 'pagoda'-form triangular).

The architectural decoration of the surviving phase includes different and unusual motifs (e.g. the grooves of the column trunks, which are not all equal, but alternately wider and narrower). This shows a moment at which a new decorative style is being elaborated, amalgamating the Italic architectural style of the Republic (as shown, for example, in the Temple of Portunus) with the influences of the Hellenistic Greek East, emphasizing the old values of Augustus's new status quo whilst showing the regime's innovative cultural credentials. This style would later be codified in the Forum of Augustus. Other new features include the insertion of decorative elements meant to celebrate Octavian, such as the laurel in the frieze and capitals.

The temple also dates from the earliest period in which marble was used in bulk for Roman public buildings, and represents a switch-over period from the traditional technologies of plastered tuff and travertine, with experimentation in ways of working with the new materials. Indeed, marble is only used on the facade, with the architects as yet uncertain of its load-bearing possibilities, as seen in the faced tuff frieze, lintel and capitals.

In the area a circular foundation and other remains suggest the colonnade of a small round building of Flavian date, which could be this temple's perirrantherion, a sacred spring used for the temple's cult (which included purification ceremonies), and later on probably for lustra.

The triumphal portico (a long portico stretching a mile between the Servian Wall's porta Carmentalis and the Trigarium) passed the corners of the temples of Apollo and Bellona, where major remains of it can be seen. Others are visible in the direction of the Capitol, along the present 'Via del Teatro di Marcello', facing the church of San Nicola in Carcere.